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Kothe Group



Biochemistry of ribosome biogenesis and tRNA maturation

Ribosome biogenesis is a complex assembly process generating the cell’s protein factories consisting of four large RNAs and more than 50 proteins. As ribosomes are of critical importance for each cell, alterations in ribosome biogenesis lead to human diseases. In order to better understand ribosome formation on a molecular level, our research focuses on the early steps of this process where only a small number of factors are involved. In particular, we study the modification of functional RNAs such as ribosomal and transfer RNA both in bacteria and eukaryotes.

By using highly purified components, we re-create this process under defined conditions in the test tube with the aim of identifying critical, limiting steps. Our approach is multi-disciplinary including molecular biology, biochemistry, biophysics and genetics allowing us to gain detailed insight into the functional cooperation of proteins and RNA in the assembly of cellular machines. Within the Alberta RNA Research and Training Institute (ARRTI), we belong to the Laboratory for structure and function of small noncoding RNAs as well as the Laboratory for biomolecular design and engineering.

Recent Publications:

  • Tillault, A.S., Fourmann, J.B., Loegler, C., Wieden, H.-J., Kothe, U., and Charpentier, B., (2015) Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and -independent pseudouridine synthase Cbf5. RNA 21, 1233-1239 DOI: 10.1261/rna.051425.115 (Impact Factor: 4.622)
  • Friedt, J., Leavens, F.M., Mercier, E., Wieden, H.-J., and Kothe, U. (2014) An arginine-aspartate network in the active site of bacterial TruB is critical for catalysing pseudouridine formation. Nucleic Acids Research, 42, 3857 - 3870 (IF: 8.808)
  • Kamalampeta, R., Keffer-Wilkes, L.C., and Kothe, U. (2013) tRNA binding, positioning and modification by the pseudouridine synthase Pus10. J. Mol. Biol., 425(20), 3863-3874 (IF: 3.959)
  • Kamalampeta, R., and Kothe, U. (2012) Archaeal proteins Nop10 and Gar1 increase the catalytic activity of Cbf5 in pseudouridylating tRNA. Scientific Reports, 2: 663, DOI: 10.1038/srep00663 (IF: 5.578)
  • Kothe, U. (2012) New frontiers in studying pseudouridine formation in RNA. Cell News (DGZ Journal) 2/2012, 48-56 (invited review)
  • Wright, J.R., Keffer-Wilkes, L.C., Dobing, S.R., and Kothe, U. (2011) Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA and RluA reveals uniformly slow catalysis. RNA, 17, 2074-2084 (IF: 4.622)
  • Kothe, U. (2010) Recent Progress on Understanding Ribosomal Protein Synthesis. In Comprehensive Natural Products II Chemistry and Biology, Section Amino Acids, Peptides and Proteins, Elsevier: Oxford, UK, 2010, Volume 5, 353-382 (invited)

Group members (Fall 2016)
Kothe group - 2016

  1. Dr. Anne Rintala-Dempsey (Research Associate)
  2. Dr. Anne-Sophie Tillault (PDF)
  3. Dr. Govardhan Reddy Veerareddygari (PDF)
  4. Evan Caton (PhD student)
  5. Abeer Ogailan (MSc student)
  6. Sarah Schultz (MSc student)
  7. Dominic Czekay (MSc student)
  8. Erin Kelly (Undergraduate)
  9. Elijah Dueck (Undergraduate)
  10. Lindey Felske (Undergraduate)
  11. Emily Soon (Research Technician)

Former Lab Members

  • Laura Keffer-Wilkes (PhD student - Summer 2012 - Summer 2016)
  • Jessica Baedke (Undergraduate - Summer 2016)
  • Alycia Amatto (Undergraduate - Summer 2015; AIHS Summer Studentship)
  • Elijah Dueck (Undergraduate - Summer 2015; NSERC USRA)
  • Jordan Stewart (Undergraduate - Spring 2015)
  • Kody Beler (Undergraduate - Spring 2015)
  • Dominic Czekay (Undergraduate - Fall 2014)
  • Erin Kelly (Undergraduate - Fall 2014)
  • Jan Tuescher (Undergraduate - Fall 2014)
  • Melanie Schwerdtfeger (Undergraduate - German Exchange Summer/Fall 2014)
  • Elijah Dueck (Undergraduate - Summer 2014; NSERC USRA)
  • Alycia Amatto (Undergraduate - Summer 2014; AIHS Summer Studentship)
  • Dominic Czekay (Undergraduate - Summer 2014; Chinook Summer Research Award)
  • Tim Vos (Undergraduate - Summer 2014)
  • Sally Xu (HYRS - Summer 2014)
  • Chris Cote (Undergraduate Fall 2013/Spring 2014)
  • Suneet Kharey (Undergraduate Fall 2013)
  • Saskia Funk (RISE - German Exchange Summer/Fall 2013)
  • Jenna Friedt (MSc Student - Fall 2011 - Summer 2013)
  • Rajashekhar Kamalampeta (PhD Student - Fall 2008 - Spring 2012)
  • Justin Luu (undergraduate)

Some Recent Successes:

  • 2015 RiboWest Poster Awards to Jessica Baedke (Undergraduate) and Sarah Schultz (Undergraduate)
  • Ute Kothe awarded Tier II Strategic Chair in Transcriptomics of RNA modification by AITF (2015-2019)
  • CIHR Synapse Mentorship Award 2012 - Individual Researcher, $ 5,000, for Ute Kothe in recognition of science outreach activities and organizing RiboWest Conferences
  • Poster award at RiboWest conference for Jenna Friedt
  • 1st Presentation Award for graduate students in Biochemistry for Jenna Friedt at 6th annual Chinook Symposium for Chemistry & Biochemistry 2012
  • Loren Hepler Gold Medal for PhD Research Excellence, second place, for Laura Keffer-Wilkes at 6th annual Chinook Symposium for Chemistry & Biochemistry 2012